phylojunction.interface package

Subpackages

• phylojunction.interface.cmdbox package
  • Submodules
  • phylojunction.interface.cmdbox.cmd_parse module
    • cmdline2dag()
    • parse_deterministic_function_assignment()
    • parse_samp_dn_assignment()
    • parse_variable_assignment()
    • script2dag()
  • phylojunction.interface.cmdbox.cmd_parse_utils module
    • parse_spec()
    • parse_val_vector()
    • tokenize_fn_spec()
    • val_or_obj()
  • Module contents
• phylojunction.interface.grammar package
  • Submodules
  • phylojunction.interface.grammar.ct_fn_grammar module
    • PJCtFnGrammar
      • PJCtFnGrammar.create_ct_fn_obj()
      • PJCtFnGrammar.ct_fn_grammar_dict
      • PJCtFnGrammar.grammar_check()
      • PJCtFnGrammar.init_return_ann_tr()
  • phylojunction.interface.grammar.ct_fn_treereader_makers module
    • make_tree_reader()
  • phylojunction.interface.grammar.det_fn_discrete_sse_makers module
    • make_DiscreteStateDependentProbability()
    • make_DiscreteStateDependentRate()
    • make_SSEStash()
  • phylojunction.interface.grammar.det_fn_grammar module
    • PJDetFnGrammar
      • PJDetFnGrammar.create_det_fn_obj()
      • PJDetFnGrammar.det_fn_grammar_dict
      • PJDetFnGrammar.grammar_check()
      • PJDetFnGrammar.init_return_sse_stash()
      • PJDetFnGrammar.init_return_state_dep_prob()
      • PJDetFnGrammar.init_return_state_dep_rate()
      • PJDetFnGrammar.init_return_tree_mapped_with_attr()
  • phylojunction.interface.grammar.det_fn_map_attribute module
    • make_mapped_ann_tree()
  • phylojunction.interface.grammar.dn_discrete_sse_makers module
    • make_discrete_SSE_dn()
  • phylojunction.interface.grammar.dn_grammar module
    • PJDnGrammar
      • PJDnGrammar.create_dn_obj()
      • PJDnGrammar.dn_grammar_dict
      • PJDnGrammar.grammar_check()
      • PJDnGrammar.init_return_discrete_SSE_dn()
      • PJDnGrammar.init_return_parametric_dn()
  • Module contents

Submodules

phylojunction.interface.pj_sandbox module

phylojunction.interface.pj_sandbox.run_example_geosse_file() → DirectedAcyclicGraph

Run example 2.

This example reads script examples/bisse.pj. The tree is a sample from a geographic state-dependent speciation extinction (GeoSSE) process.

phylojunction.interface.pj_sandbox.run_example_manual_incomplete_sampling_bisse() → DirectedAcyclicGraph

Run example 3.

This example manually builds a BiSSE distribution with incomplete sampling, assigns it to a stochastic DAG node, and adds the node to a DAG.

phylojunction.interface.pj_sandbox.run_example_manual_tree_building(ax: Axes) → None

Run example 4.

This example manually builds an AnnotatedTree instance manually and plots it on provided Axes object.

phylojunction.interface.pj_sandbox.run_example_map_attr(ax: Axes) → None

Run example 6.

Returns:

phylojunction.interface.pj_sandbox.run_example_read_tree_function(ax: Axes) → None

Run example 5.

This example reads a newick string into an AnnotatedTree instance, and plots it in the provided Axes object.

phylojunction.interface.pj_sandbox.run_example_yule_string() → DirectedAcyclicGraph

Run example 1.

This example sets up a simple Yule model with two samples, and two Yule tree replicates per sample.

Module contents